Abstract
BackgroundShort chain dehydrogenases/reductases (SDR) are NAD(P)(H)-dependent oxidoreductases with a highly conserved 3D structure and of an early origin, which has allowed them to diverge into several families and enzymatic activities. The SDR196C family (http://www.sdr-enzymes.org) groups bacterial sorbitol dehydrogenases (SDH), which are of great industrial interest. In this study, we examine the phylogenetic relationship between the members of this family, and based on the findings and some sequence conserved blocks, a new and a more accurate classification is proposed.ResultsThe distribution of the 66 bacterial SDH species analyzed was limited to Gram-negative bacteria. Six different bacterial families were found, encompassing α-, β- and γ-proteobacteria. This broad distribution in terms of bacteria and niches agrees with that of SDR, which are found in all forms of life. A cluster analysis of sorbitol dehydrogenase revealed different types of gene organization, although with a common pattern in which the SDH gene is surrounded by sugar ABC transporter proteins, another SDR, a kinase, and several gene regulators.According to the obtained trees, six different lineages and three sublineages can be discerned. The phylogenetic analysis also suggested two different origins for SDH in β-proteobacteria and four origins for γ-proteobacteria.Finally, this subdivision was further confirmed by the differences observed in the sequence of the conserved blocks described for SDR and some specific blocks of SDH, and by a functional divergence analysis, which made it possible to establish new consensus sequences and specific fingerprints for the lineages and sub lineages.ConclusionSDH distribution agrees with that observed for SDR, indicating the importance of the polyol metabolism, as an alternative source of carbon and energy. The phylogenetic analysis pointed to six clearly defined lineages and three sub lineages, and great variability in the origin of this gene, despite its well conserved 3D structure. This suggests that SDH are very old and emerged early during the evolution. This study also opens up a new and more accurate classification of SDR196C family, introducing two numbers at the end of the family name, which indicate the lineage and the sublineage of each member, i.e, SDR196C6.3.
Highlights
Short chain dehydrogenases/reductases (SDR) are NAD(P)(H)-dependent oxidoreductases with a highly conserved 3D structure and of an early origin, which has allowed them to diverge into several families and enzymatic activities
The sorbitol dehydrogenases (SDH) gene was found in 66 bacterial species, all of them Gramnegative belonging to alpha (α), beta (β)- and gamma (γ)-Proteobacteria, with both low and high GC representatives
The Acetobacteriaceae family is represented by two members, Acidiphilium cryptum and Gluconoacetobacter hansenii, which are common in vinegar and used as iron contamination indicators [20]
Summary
Short chain dehydrogenases/reductases (SDR) are NAD(P)(H)-dependent oxidoreductases with a highly conserved 3D structure and of an early origin, which has allowed them to diverge into several families and enzymatic activities. Among SDR, no high sequence identity between different members is observed (about 20–30%), but all of them display a highly similar 3D structure, typically folding into a simple one-domain architecture with distinct conserved motifs, including the cofactor binding site at the N-terminal, structure stabilizing motifs, the active center, catalysis-enhancing sites and the substrate binding site, located in the highly variable C-terminal region [1,11]. Based on the similar coenzyme-binding structure, their active-site relationship and repetitive patterns, five SDR superfamily types have been discerned from different data banks, named as “classical”, “extended”, “intermediate”, “divergent” and “complex” SDR enzymes [12]. This divergence includes different enzymatic activities, most of them dehydrogenases or reductases, and lyases and some isomerases.
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